John A. Kirkegaard

MYC2 Differentially Modulates Diverse Jasmonate-Dependent Functions in Arabidopsis

The Arabidopsis thaliana basic helix-loop-helix Leu zipper transcription factor (TF) MYC2/JIN1 differentially regulates jasmonate (JA)-responsive pathogen defense (e.g., PDF1.2) and wound response (e.g., VSP) genes. In this study, genome-wide transcriptional profiling of wild type and mutant myc2/jin1 plants followed by functional analyses has revealed new roles for MYC2 in the modulation of diverse JA functions. We found that MYC2 negatively regulates Trp and Trp-derived secondary metabolism such as indole glucosinolate biosynthesis during JA signaling. Furthermore, MYC2 positively regulates JA-mediated resistance to insect pests, such as Helicoverpa armigera, and tolerance to oxidative stress, possibly via enhanced ascorbate redox cycling and flavonoid biosynthesis. Analyses of MYC2 cis binding elements and expression of MYC2-regulated genes in T-DNA insertion lines of a subset of MYC2–regulated TFs suggested that MYC2 might modulate JA responses via differential regulation of an intermediate spectrum of TFs with activating or repressing roles in JA signaling. MYC2 also negatively regulates its own expression, and this may be one of the mechanisms used in fine-tuning JA signaling. Overall, these results provide new insights into the function of MYC2 and the transcriptional coordination of the JA signaling pathway.

Biofumigation potential of brassicas

Isothiocyanates (ITCs) released from Brassica crops or seed meal amendments incorporated into soil have the potential to suppress pest and disease organisms in soil. We investigated in vitro toxicity of six ITCs to the mycelial growth of five cereal root pathogens (Gaeumannomyces graminis var. tritici, Rhizoctonia solani, Fusarium graminearum, Bipolaris sorokiniana, Pythium irregulare) by either adding them to the headspace above, or dissolving them in the growing media. Four alkenyl aliphatic ITCs (methyl-ITC, propenyl-ITC, butenyl-ITC, pentenyl-ITC) and two aromatic ITCs (benzyl-ITC and 2-phenylethyl-ITC) were tested. Aromatic ITCs were less toxic in the headspace experiments due to their lower volatility which reduced the headspace concentration, but were more toxic than the aliphatic ITCs when dissolved in the agar. In both experimental methods, the toxicity of the aliphatic ITCs decreased with increasing length of the side chain although there was little difference between methyl-ITC and propenyl-ITC in the headspace experiment. The fungi differed in sensitivity to the ITCs. Gaeumannomyces was the most sensitive, Rhizoctonia and Fusarium intermediate and Bipolaris and Pythium the least sensitive. Pythium was 2–16 times more resistant than the other fungi to the ITCs dissolved in agar and, in contrast to the other fungi, was more sensitive to the aliphatic ITCs than the aromatic ITCs. Suppression of some fungi by propenyl ITC and 2-phenylethyl ITC, principal products of glucosinolate hydrolysis in Brassica tissue, was superior to that of the synthetic fumigant methyl-ITC, suggesting an important role for these compounds in the pest suppression potential of brassicas. The variation in toxicity of different ITCs to the fungi (up to 7 fold) suggests there is significant scope to enhance the biofumigation potential of brassicas by selecting those which produce large quantities of GSL precursors to the most toxic ITCs for the target organism.

Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops

Wheat yields globally will depend increasingly on good management to conserve rainfall and new varieties that use water efficiently for grain production. Here we propose an approach for developing new varieties to make better use of deep stored water. We focus on water-limited wheat production in the summer-dominant rainfall regions of India and Australia, but the approach is generally applicable to other environments and root-based constraints. Use of stored deep water is valuable because it is more predictable than variable in-season rainfall and can be measured prior to sowing. Further, this moisture is converted into grain with twice the efficiently of in-season rainfall since it is taken up later in crop growth during the grain-filling period when the roots reach deeper layers. We propose that wheat varieties with a deeper root system, a redistribution of branch root density from the surface to depth, and with greater radial hydraulic conductivity at depth would have higher yields in rainfed systems where crops rely on deep water for grain fill. Developing selection systems for mature root system traits is challenging as there are limited high-throughput phenotyping methods for roots in the field, and there is a risk that traits selected in the lab on young plants will not translate into mature root system traits in the field. We give an example of a breeding programme that combines laboratory and field phenotyping with proof of concept evaluation of the trait at the beginning of the selection programme. This would greatly enhance confidence in a high-throughput laboratory or field screen, and avoid investment in screens without yield value. This approach requires careful selection of field sites and years that allow expression of deep roots and increased yield. It also requires careful selection and crossing of germplasm to allow comparison of root expression among genotypes that are similar for other traits, especially flowering time and disease and toxicity resistances. Such a programme with field and laboratory evaluation at the outset will speed up delivery of varieties with improved root systems for higher yield.

Biofumigation and Enhanced Biodegradation: Opportunity and Challenge in Soilborne Pest and Disease Management

Management of soilborne pests and diseases in cropping systems is often highly challenging—in implementation of acceptable methodologies and in dealing with secondary problems. The phase-out of methyl bromide brings this into particularly sharp focus. There is a need for diversified options and alternatives to fill different roles across the soilborne pest and disease management spectrum, but flexibility is limited, as practicalities demand that they fit into a prophylactic methodology. It is against such a backdrop that expectations and promotion of alternatives must be set. There is also a need to recognize potentially serious problems that may have been masked under historical management regimes, but for which the nature of the system offers little scope to avoid or manage. Biofumigation is the beneficial use of Brassica green manures that release isothiocyanates chemically similar to methyl isothiocyanate, the active agent from the synthetic fumigant metam sodium, which is used as a substitute for methyl bromide in some systems. A systematic approach to research into biofumigation, specifically aimed at overcoming a long history of empiricism, has seen significant recent advances in both basic and applied knowledge. A key development has been achievement of maximal biofumigation potential through greatly enhanced release of appropriate isothiocyanates into soil. These advances have led to commercial adoption, demonstrating that biofumigation, when applied to appropriate production systems, can have efficacy and offer cost savings. Crucially, these systematically derived research and development findings and their adoption now provide the impetus for self-sustaining further development and market penetration of the concept. Despite this success, biofumigation is not seen as being sufficiently powerful or practical in implementation to be an alternative to methyl bromide on a broad scale and misdirection in that regard could be counterproductive to more appropriately targeted further development. Enhanced microbial biodegradation is a cryptic phenomenon that can diminish the efficacy of soil-applied pesticides, including isothiocyanates and most other currently available methyl bromide substitutes. Because methyl bromide is not susceptible, the phenomenon has potentially serious implications in intensive production systems switching from methyl bromide to reliance on other compounds that are. It is an intractable problem once induced. Avoidance of its onset is the only feasible management strategy. This has been aided for some particularly vulnerable environments by recent clarification of key risk factors associated with soil type, soil pH, and calcium content.

Biofumigation: Isothiocyanates released from Brassica roots inhibit growth of the take-all fungus

The presence of root tissue of the brassicas canola and Indian mustard inhibited growth of pure cultures of the fungal pathogen which causes take-all of wheat [Gaeumannomyces graminis (Sacc.) Arx and Oliver var.tritici, abbreviated as Ggt]. Ggt growth was generally inhibited more in the presence of Indian mustard roots than canola roots. Dried irradiated roots were consistently effective in reducing Ggt growth, but growth inhibition by young live roots and macerated roots was not consistent. The inhibitory compound(s) were shown to be volatile because the symmetry of Ggt growth was not affected by the proximity of theBrassica tissue. Volatile breakdown products from maceratedBrassica roots were identified using a gas chromatograph-mass spectrometer. The major compounds found were isothiocyanates (ITCs). Canola roots released mostly methyl ITC and Indian mustard roots released mostly phenylethyl ITC. Low concentrations of these and related compounds inhibited growth of Ggt in pure culture when supplied as the vapour of pure chemicals in concentrations within the range expected during breakdown ofBrassica roots in soil.

Impact of subsoil water use on wheat yield

Water stored deep in the soil profile is generally considered valuable to crop yield because it becomes available during grain filling, but the value of subsoil water for grain yield has not been isolated and quantified in the field. We used rainout shelters with irrigation to control the water supply to wheat crops that had different amounts of subsoil water available to isolate and quantify the efficiency with which the subsoil water was converted to grain yield. Under moderate post-anthesis stress, 10.5 mm of additional subsoil water used in the 1.35-1.85 m layer after anthesis increased grain yield by 0.62 t/ha, representing an efficiency of 59 kg/ha.mm. The additional yield resulted from a period of higher assimilation 12-27 days after anthesis and was related to an increase in grain size rather than other yield components. Under more severe stress with earlier onset, extra water use below 1.25 m was accompanied by additional water use in upper soil layers and it was more difficult to isolate and quantify the benefit of deep water to grain yield. The additional water used from all layers from the time the stress was imposed was converted to grain at 30-40 kg/ha.mm, but this increased to 60 kg/ha.mm for water used after anthesis. The high efficiency for subsoil water use is 3 times that typically expected for total seasonal water use, and twice that previously estimated for total post-anthesis water use in a similar environment. The results demonstrate that relatively small amounts of subsoil water can be highly valuable to grain yield.

The distribution and abundance of wheat roots in a dense, structured subsoil – implications for water uptake

We analysed the abundance, spatial distribution and soil contact of wheat roots in dense, structured subsoil to determine whether incomplete extraction of subsoil water was due to root system limitations. Intact soil cores were collected to 1.6 m below wheat crops at maturity on a red Kandosol in southern Australia. Wheat roots, remnant roots, soil pores and root-soil contact were quantified at fresh breaks in the soil cores. In surface soil layers (<0.6 m) 30-40% of roots were clumped within pores and cracks in the soil, increasing to 85-100% in the subsoil (>0.6 m), where 44% of roots were in pores with at least three other roots. Most pores contained no roots, with occupancy declining from 20% in surface layers to 5% in subsoil. Wheat roots clumped into pores contacted the surrounding soil via numerous root hairs, whereas roots in cracks were appressed to the soil surface and had very few root hairs. Calculations assuming good root-soil contact indicated that root density was sufficient to extract available subsoil water, suggesting that uptake is constrained at the root-soil interface. To increase extraction of subsoil water, genetic targets could include increasing root-soil contact with denser root hairs, and increasing root proliferation to utilize existing soil pores.

Root and shoot glucosinolates: a comparison of their diversity, function and interactions in natural and managed ecosystems

The role of glucosinolates in aboveground plant–insect and plant–pathogen interactions has been studied widely in both natural and managed ecosystems. Fewer studies have considered interactions between root glucosinolates and soil organisms. Similarly, data comparing local and systemic changes in glucosinolate levels after root- and shoot-induction are scarce. An analysis of 74 studies on constitutive root and shoot glucosinolates of 29 plant species showed that overall, roots have higher concentrations and a greater diversity of glucosinolates than shoots. Roots have significantly higher levels of the aromatic 2-phenylethyl glucosinolate, possibly related to the greater effectiveness and toxicity of its hydrolysis products in soil. In shoots, the most dominant indole glucosinolate is indol-3-ylglucosinolate, whereas roots are dominated by its methoxyderivatives. Indole glucosinolates were the most responsive after jasmonate or salicylate induction, but increases after jasmonate induction were most pronounced in the shoot. In general, root glucosinolate levels did not change as strongly as shoot levels. We postulate that roots may rely more on high constitutive levels of glucosinolates, due to the higher and constant pathogen pressure in soil communities. The differences in root and shoot glucosinolate patterns are further discussed in relation to the molecular regulation of glucosinolate biosynthesis, the within-tissue distribution of glucosinolates in the roots, and the use of glucosinolate-containing crops for biofumigation. Comparative studies of tissue-specific biosynthesis and regulation in relation to the biological interactions in aboveground and belowground environments are needed to advance investigations of the evolution and further utilization of glucosinolates in natural and managed ecosystems.

Increasing productivity by matching farming system management and genotype in water-limited environments

Improvements in water productivity and yield arise from interactions between varieties (G) and their management (M). Most G×M interactions considered by breeders and physiologists focus on in-crop management (e.g. sowing time, plant density, N management). However, opportunities exist to capture more water and use it more effectively that involve judicious management of prior crops and fallows (e.g. crop sequence, weed control, residue management). The dry-land wheat production system of southern Australia, augmented by simulation studies, is used to demonstrate the relative impacts and interactions of a range of pre-crop and in-crop management decisions on water productivity. A specific case study reveals how a novel genetic trait, long coleoptiles that enable deeper sowing, can interact with different management options to increase the water-limited yield of wheat from 1.6 t ha(-1) to 4.5 t ha(-1), reflecting the experience of leading growers. Understanding such interactions will be necessary to capture benefits from new varieties within the farming systems of the future.

Comparison of canola, Indian mustard and Linola in two contrasting environments. I. Effects of nitrogen fertilizer on dry-matter production, seed yield and seed quality

Abstract The potential for extending the production of winter oilseed crops into the drier region of the cereal belt of eastern Australia was examined by comparing canola, Indian mustard and Linola in field experiments in the contrasting environments of Junee and Condobolin, NSW. Junee is in the region where canola production is concentrated, and Condodolin is in the drier part of the cereal belt currently considered marginal for canola. Different rates of nitrogen (N) fertilizer were applied in all experiments, and there were two times of sowing at Condobolin. Wheat was grown for comparison in all experiments. Crop performance was evaluated over two seasons by measuring dry-matter production, grain yield, water-use efficiency, and seed oil and protein contents. Maximum grain yields of all crops at Junee were higher than at Condobolin, and yield responses to N fertilizer in both environments were greater in the wetter 1992 season than in the drier 1991 season. Canola and wheat showed the largest yield responses to N fertilizer, but Linola generally had the lowest yield responses because of poor seedling emergence at high N rates, intolerance of drought during grain filling (1991) and lodging (1992). Based on the overall growth and grain yield responses to N fertilizer, and on N (protein) removal in grain, it is suggested that about 25% more N be applied to canola than to wheat, that Indian mustard receive about the same N fertilizer rate as wheat, and that Linola requires about 20% less N than wheat. Sowing late at Condobolin, when there was below-average rainfall during grain filling (1991) reduced the yield of canola and Linola, but not Indian mustard. There was no yield penalty for sowing the crops late in 1992 when conditions were favourable during grain filling. Grain harvest indices based either on dry matter or the biosynthetic cost of seed production were higher for wheat and canola than for Indian mustard and Linola, and were largely unaffected by the N treatments. A potential transpiration efficiency value of 12.5 kg seed ha −1 mm −1 was derived for the oilseeds based on the biosynthetic costs of seed production. Oil concentrations were reduced by dry conditions during seed filling, by late sowing and by N fertilizer. Oil concentrations were higher at Junee than Condobolin, due mainly to differences in ambient temperature as there was a 2.7% decrease in oil concentration for each 1°C rise in mean temperature during seed filling. Oilseed meal and wheat grain protein levels were more responsive to N fertilizer when conditions were dry during grain filling. Protein levels in oilseed meals were higher but wheat grain protein was lower when conditions were favourable during grain filling. The study indicated that there are prospects for extending the production of canola and Indian mustard into drier regions of the cereal belt because, when sown early, they have similar water-use efficiencies to wheat based on the biosynthetic costs of grain production. While the yield of Indian mustard is limited by a low harvest index, its yield stability under dry post-anthesis conditions indicates greater potential than current canola cultivars for more marginal areas. Linola showed the least potential as an oilseed for the drier parts of the cereal belt because of shallow rooting and susceptibility to drought.